Blood brain barrier in AD - Sequencing the blood brain barrier in AD

Plan

background info in vascular stuff (small vessel disease)
study design
results
plan for BHF project

Glossery

Infarction: tissue death due to inadequate blood supply
- Result of prolonged ischaemia, typically due to an artery blockage, rupture or vasoconstriction
- Resulting lesion is refereed to as an infarct
Ischaemia: insufficient supply of oxygen/nutrition to tissue due to disrupted blood supply

Vascular dementia

Second most common dementia (~15-30%), and most common secondary dementia
Post-stroke 15-30% subjects develop dementia (Pendlebury and Rothwell 2009)
- Some argue should be viewed as a subtype due to differing pathophysiology

Image depicting 4 MRI brain scans with various vascular damage

Structure of the neurovasculature

An image depicting the cellular structure of the blood vessels in the brain.

Vascular segmentation

An image depicting the cellular segmentation of a blood vessel in the brain

Study design

20 cases + 20 controls post-mortem human brain tissue
Parenchyma and vascular fractions (80 samples total) > single cell seq
Genotyping pending

A cartoon deliniating the parenchyma and vascular components of the brain — Adapted from Warren (2018)

Data procesing

Using scflow

PCA/UMAP

Inverted example slide

Here is some text. The font is Arial (hex: #00326e). Here is another sentence with bold and italic text.

Here is a bullet point
The font used is Arial and font size is 18px
Bullets are coloured hex: #0ac8ff

Content here for tabset 1 :)

Incremental content

Hi!

Use . . . to separate content as an incremental slide!

Examples with R code: Plots

## make a plot
ggplot(diamonds, aes(carat, price, colour = cut)) +
    geom_point() +
    theme_bw() +
    scale_color_viridis_d()

Examples with R code: Tables

## print table
diamonds %>%
  slice_sample(n = 10) %>%
  gt() %>%
  tab_header(title = md("**Table title**"), subtitle = md("A *subtitle*")) %>%
  tab_source_note("Here is some source information")

carat	cut	color	clarity	depth	table	price	x	y	z
Table title
A subtitle
1.02	Ideal	D	SI1	62.3	56	5266	6.49	6.45	4.03
0.34	Ideal	E	VS1	60.8	57	1033	4.53	4.49	2.74
0.31	Ideal	G	SI2	60.5	57	523	4.40	4.36	2.65
1.50	Very Good	G	SI2	63.1	57	9282	7.29	7.25	4.59
1.23	Ideal	H	VS2	62.8	56	7900	6.76	6.84	4.27
1.55	Ideal	J	SI1	61.7	54	7987	7.47	7.50	4.62
1.01	Very Good	D	SI2	62.9	59	4064	6.29	6.37	3.98
0.30	Ideal	F	VS1	61.8	55	612	4.31	4.33	2.67
0.61	Premium	F	VVS1	61.8	59	2753	5.48	5.40	3.36
0.30	Ideal	H	VS1	61.6	57	526	4.30	4.33	2.66
Here is some source information

Examples with R code: HTML Widgets

leaflet() %>% 
  addTiles() %>% 
  setView(-0.1371784166832623, 51.52405283300594, zoom = 17)

Examples with R code: HTML Widgets 2

DT::datatable(head(iris, 10), fillContainer = FALSE,
              options = list(pageLength = 6))

Example with R code: Math expressions

You can write LaTeX math expressions inside a pair of dollar signs, e.g. $\alpha+\beta$ renders $\alpha+\beta$. You can use the display style with double dollar signs:

$$\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i$$

\[\bar{X}=\frac{1}{n}\sum_{i=1}^nX_i\]

Diagrams with Mermaid!

Read about how to create a diagram in this post by Mine Çetinkaya-Rundel.

flowchart LR
  A[qmd] --> B(Knitr)
  A[qmd] --> C(Jupyter)
  B(Knitr) --> D[md]
  C(Jupyter) --> D[md]
  D[md] --> E(pandoc)
  E(pandoc) --> F(HTML)
  E(pandoc) --> G(PDF)
  E(pandoc) --> H(Word)
  E(pandoc) --> I{and more}

Figure 1: How Quarto orchestrates rendering of documents: start with a qmd file, use the Knitr or Jupyter engine to perform the computations and convert it to an md file, then use Pandoc to convert to various file formats including HTML, PDF, and Word.

Exporting into PDF

You can use the function pagedown::chrome_print() to print the HTML version into a PDF!

pagedown::chrome_print("path-to-file.html")

Thanks for listening

Replace profile.png with the path to the pictures you’d like to use.

Name Porsition/Role

Collaborator institution
Name (Position/Role)
Name (Position/Role)
Name (Position/Role)

References

Pendlebury, Sarah T., and Peter M. Rothwell. 2009. “Prevalence, Incidence, and Factors Associated with Pre-Stroke and Post-Stroke Dementia: A Systematic Review and Meta-Analysis.” The Lancet Neurology 8 (11): 1006–18. https://doi.org/10.1016/S1474-4422(09)70236-4.

Schaeffer, Samantha, and Costantino Iadecola. 2021. “Revisiting the Neurovascular Unit.” Nature Neuroscience 24 (9): 1198–1209. https://doi.org/10.1038/s41593-021-00904-7.

Warren, Katherine Elizabeth. 2018. “Beyond the Blood:Brain Barrier: The Importance of Central Nervous System (CNS) Pharmacokinetics for the Treatment of CNS Tumors, Including Diffuse Intrinsic Pontine Glioma.” Frontiers in Oncology 8.